Discrepant cytogenetic, MLPA and array CGH results on a der(X)(pter->q27.2::p22.31->pter): the
advantages of an integrated approach.
• M N Collinson, S Huang, JN Macpherson, VK Maloney, AC Skinner, A Karcanias, NA Affara, NS Thomas
30 year old female with premature ovarian failure (POF)
cytogenetic analysis molecular genetic testing for a FRAXA premutation
46,XX only one allele found?45,X or 46,XY
LIST OF PROBES USED FOR FISH TO CONFIRM DELETIONCentromere
RP1-142F18 Normal (Xq27.2)
RP1-315J21 Deleted (Xq27.3)
RP11-79A21 Deleted (Xq27.3)
RP11-37P24 Deleted (fragile X locus)
RP11-161L9 Deleted (fragile X locus)
RP11-64L19 Deleted (Xq28)
RP11-533H4 Deleted (Xq28)
RP11-76K17 Deleted (Xq28)
RP11-402H20 Deleted (Xq28)
Telomere
Analyst Slide
1
Slide
2
Slide
3
Slide
4
Slide
5
Slide
6
1 X
2 X
3 X
Blind cytogenetic analysis – 3 control slides and 3 slides from POF patient scored by 3 independent analysts
FEMALE CONTROL MALE CONTROL
Array CGH with chip specifically designed for sex chromosome abnormalities
NORMAL CASE
FEMALE CONTROL MALE CONTROL
Array CGH with chip specifically designed for sex chromosome abnormalities
POF CASE
Original cytogenetic analysis – 1/30 metaphases 45,X
Blind FISH study with X centromere probe (DXZ2)
Metaphases
Interphase cells
POF case Control
1/30 45,X (3.3%) 1/30 45,X (3.3%)
8/100 45,X (8%) 6/100 45,X (6%)
Summary• An integrated approach was required to establish the
true nature of the X chromosome abnormality
• Highlights the fact that one should be cautious of any shifts from the baseline when analysing array CGH as it may mask significant changes in log ratios
• We still do not have a satisfactory explanation of our results other than mosaicism
• Deletions of this region of Xq have been reported in association with POF